Genomic level sequencing is increasingly affordable and accessible, allowing us to explore the population genetics and phylogeography of non-model taxa with previously unimaginable datasets. Population genomic studies using RAD (restriction site-associated DNA) sequencing is an alternative to traditional microsatellite and Sanger sequencing methods and has the advantage of requiring fewer individual samples whilst still producing powerful datasets. The genetic structure of most Australian desert mammals is poorly understood, in part because it is difficult to obtain enough samples for population genetic studies. Survey work in the arid Pilbara, Western Australia, in 2003-2006 provides a large repository of high quality mammal tissues held at the WA Museum suitable for RAD sequencing. In this comparative study we sequenced the two commonly used mitochondrial genes from two endemic Pilbara planigales (Dasyuromorphia), one species a generalist that is commonly captured at most survey sites and the other restricted to cracking clay habitats. Contrary to expectations, clear genetic structure was detected in the mtDNA data for the generalist species but not for the habitat specialist. A sub-set of these individuals, selected continuously throughout the species distributions, were then used for RAD sequencing. With the more powerful RAD sequencing dataset clear population structure was evident for both species. We compare the results from the two methods and show that RAD sequencing is a useful tool for investigating the population structure of desert and rare mammals where sufficient high-quality DNA samples are available.